rs2600003

Organism: Homo sapiens

Alleles: A>C / A>T

Gene : Feature

KIF5A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0058 (1748/29972,GnomAD)
C=0074 (2177/29118,TOPMED)
C=0059 (296/5008,1000G)
C=0028 (108/3854,ALSPAC)
C=0027 (100/3708,TWINSUK)

Position: chr12:57559461 (GRCh38.p7) (12q13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 Enhancers around

Promoter: 104 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.57559461A>C
GRCh38.p7 chr 12	NC_000012.12:g.57559461A>T
GRCh37.p13 chr 12	NC_000012.11:g.57953244A>C
GRCh37.p13 chr 12	NC_000012.11:g.57953244A>T
KIF5A RefSeqGene	NG_008155.1:g.14398A>C
KIF5A RefSeqGene	NG_008155.1:g.14398A>T

Gene: KIF5A, kinesin family member 5A(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KIF5A transcript	NM_004984.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.872	C=0.128
1000Genomes	American	Sub	694	A=0.980	C=0.020
1000Genomes	East Asian	Sub	1008	A=1.000	C=0.000
1000Genomes	Europe	Sub	1006	A=0.950	C=0.050
1000Genomes	Global	Study-wide	5008	A=0.941	C=0.059
1000Genomes	South Asian	Sub	978	A=0.940	C=0.060
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.972	C=0.028
The Genome Aggregation Database	African	Sub	8724	A=0.892	C=0.108
The Genome Aggregation Database	American	Sub	838	A=0.970	C=0.03,
The Genome Aggregation Database	East Asian	Sub	1622	A=0.999	C=0.001
The Genome Aggregation Database	Europe	Sub	18486	A=0.958	C=0.041
The Genome Aggregation Database	Global	Study-wide	29972	A=0.941	C=0.058
The Genome Aggregation Database	Other	Sub	302	A=0.960	C=0.04,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.925	C=0.074
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.973	C=0.027

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2600003	0.00018	alcohol dependence	20201924

eQTL of rs2600003 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs2600003 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr12	57910447	57911081	E067	-31224
chr12	57911093	57911330	E067	-30975
chr12	57911348	57911490	E067	-30815
chr12	57911504	57911591	E067	-30714
chr12	57918415	57919003	E067	-23302
chr12	57941538	57941615	E067	-690
chr12	57942846	57943177	E067	541
chr12	57989615	57989655	E067	47310
chr12	57989691	57989741	E067	47386
chr12	57911093	57911330	E068	-30975
chr12	57911348	57911490	E068	-30815
chr12	57911504	57911591	E068	-30714
chr12	57919004	57919195	E068	-23110
chr12	57919198	57919312	E068	-22993
chr12	57919329	57919413	E068	-22892
chr12	57929056	57929165	E068	-13140
chr12	57929382	57929462	E068	-12843
chr12	57929508	57929639	E068	-12666
chr12	57937337	57937458	E068	-4847
chr12	57937463	57937751	E068	-4554
chr12	57937883	57937951	E068	-4354
chr12	57938775	57938892	E068	-3413
chr12	57946085	57946151	E068	3780
chr12	57946312	57946362	E068	4007
chr12	57911093	57911330	E069	-30975
chr12	57911348	57911490	E069	-30815
chr12	57918415	57919003	E069	-23302
chr12	57919004	57919195	E069	-23110
chr12	57919198	57919312	E069	-22993
chr12	57937337	57937458	E069	-4847
chr12	57937463	57937751	E069	-4554
chr12	57937883	57937951	E069	-4354
chr12	57938775	57938892	E069	-3413
chr12	57918415	57919003	E070	-23302
chr12	57919004	57919195	E070	-23110
chr12	57919198	57919312	E070	-22993
chr12	57919329	57919413	E070	-22892
chr12	57919497	57919547	E070	-22758
chr12	57919596	57919669	E070	-22636
chr12	57919727	57920070	E070	-22235
chr12	57920074	57920277	E070	-22028
chr12	57920377	57920427	E070	-21878
chr12	57920470	57920903	E070	-21402
chr12	57937337	57937458	E070	-4847
chr12	57937463	57937751	E070	-4554
chr12	57938775	57938892	E070	-3413
chr12	57948692	57948811	E070	6387
chr12	57948820	57948870	E070	6515
chr12	57950684	57950748	E070	8379
chr12	57986304	57986681	E070	43999
chr12	57986737	57986941	E070	44432
chr12	57987016	57987056	E070	44711
chr12	57911348	57911490	E071	-30815
chr12	57911504	57911591	E071	-30714
chr12	57937337	57937458	E071	-4847
chr12	57937463	57937751	E071	-4554
chr12	57937883	57937951	E071	-4354
chr12	57938775	57938892	E071	-3413
chr12	57941538	57941615	E071	-690
chr12	57942846	57943177	E071	541
chr12	57947093	57947283	E071	4788
chr12	57910447	57911081	E072	-31224
chr12	57911093	57911330	E072	-30975
chr12	57911348	57911490	E072	-30815
chr12	57911504	57911591	E072	-30714
chr12	57911874	57912541	E072	-29764
chr12	57937337	57937458	E072	-4847
chr12	57937463	57937751	E072	-4554
chr12	57937883	57937951	E072	-4354
chr12	57938775	57938892	E072	-3413
chr12	57910447	57911081	E073	-31224
chr12	57911093	57911330	E073	-30975
chr12	57911348	57911490	E073	-30815
chr12	57911504	57911591	E073	-30714
chr12	57918415	57919003	E073	-23302
chr12	57919004	57919195	E073	-23110
chr12	57919198	57919312	E073	-22993
chr12	57919329	57919413	E073	-22892
chr12	57919497	57919547	E073	-22758
chr12	57919596	57919669	E073	-22636
chr12	57919727	57920070	E073	-22235
chr12	57920074	57920277	E073	-22028
chr12	57937337	57937458	E073	-4847
chr12	57937463	57937751	E073	-4554
chr12	57937883	57937951	E073	-4354
chr12	57918415	57919003	E074	-23302
chr12	57918415	57919003	E081	-23302
chr12	57919004	57919195	E081	-23110
chr12	57919198	57919312	E081	-22993
chr12	57919329	57919413	E081	-22892
chr12	57919497	57919547	E081	-22758
chr12	57919596	57919669	E081	-22636
chr12	57919727	57920070	E081	-22235
chr12	57920074	57920277	E081	-22028
chr12	57938775	57938892	E081	-3413
chr12	57942846	57943177	E081	541
chr12	57946312	57946362	E081	4007
chr12	57946408	57946458	E081	4103
chr12	57946495	57946547	E081	4190
chr12	57948692	57948811	E081	6387
chr12	57948820	57948870	E081	6515
chr12	57950250	57950469	E081	7945
chr12	57986304	57986681	E081	43999
chr12	57986737	57986941	E081	44432
chr12	57987016	57987056	E081	44711
chr12	57987138	57987204	E081	44833
chr12	57918415	57919003	E082	-23302
chr12	57919004	57919195	E082	-23110
chr12	57919198	57919312	E082	-22993
chr12	57919329	57919413	E082	-22892
chr12	57919497	57919547	E082	-22758
chr12	57919596	57919669	E082	-22636
chr12	57919727	57920070	E082	-22235
chr12	57937337	57937458	E082	-4847
chr12	57937463	57937751	E082	-4554
chr12	57937883	57937951	E082	-4354
chr12	57938775	57938892	E082	-3413
chr12	57948692	57948811	E082	6387
chr12	57948820	57948870	E082	6515

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	57912852	57915051	E067	-27254
chr12	57939511	57941533	E067	-772
chr12	57943248	57944621	E067	943
chr12	57944681	57944857	E067	2376
chr12	57944886	57945001	E067	2581
chr12	57945065	57945105	E067	2760
chr12	57945115	57945274	E067	2810
chr12	57945433	57945560	E067	3128
chr12	57945589	57945751	E067	3284
chr12	57945845	57945940	E067	3540
chr12	57947293	57947404	E067	4988
chr12	57984184	57986177	E067	41879
chr12	57912852	57915051	E068	-27254
chr12	57939511	57941533	E068	-772
chr12	57943248	57944621	E068	943
chr12	57944681	57944857	E068	2376
chr12	57944886	57945001	E068	2581
chr12	57945065	57945105	E068	2760
chr12	57945115	57945274	E068	2810
chr12	57945433	57945560	E068	3128
chr12	57945589	57945751	E068	3284
chr12	57947293	57947404	E068	4988
chr12	57984184	57986177	E068	41879
chr12	57912852	57915051	E069	-27254
chr12	57939511	57941533	E069	-772
chr12	57943248	57944621	E069	943
chr12	57944681	57944857	E069	2376
chr12	57944886	57945001	E069	2581
chr12	57945065	57945105	E069	2760
chr12	57945115	57945274	E069	2810
chr12	57945433	57945560	E069	3128
chr12	57945589	57945751	E069	3284
chr12	57945845	57945940	E069	3540
chr12	57947293	57947404	E069	4988
chr12	57984184	57986177	E069	41879
chr12	57912852	57915051	E070	-27254
chr12	57939511	57941533	E070	-772
chr12	57943248	57944621	E070	943
chr12	57944681	57944857	E070	2376
chr12	57944886	57945001	E070	2581
chr12	57945065	57945105	E070	2760
chr12	57945115	57945274	E070	2810
chr12	57945433	57945560	E070	3128
chr12	57945589	57945751	E070	3284
chr12	57945845	57945940	E070	3540
chr12	57947293	57947404	E070	4988
chr12	57984184	57986177	E070	41879
chr12	57912852	57915051	E071	-27254
chr12	57939511	57941533	E071	-772
chr12	57943248	57944621	E071	943
chr12	57944681	57944857	E071	2376
chr12	57984184	57986177	E071	41879
chr12	57912852	57915051	E072	-27254
chr12	57939511	57941533	E072	-772
chr12	57943248	57944621	E072	943
chr12	57944681	57944857	E072	2376
chr12	57944886	57945001	E072	2581
chr12	57945065	57945105	E072	2760
chr12	57945115	57945274	E072	2810
chr12	57945433	57945560	E072	3128
chr12	57945589	57945751	E072	3284
chr12	57945845	57945940	E072	3540
chr12	57947293	57947404	E072	4988
chr12	57984184	57986177	E072	41879
chr12	57912852	57915051	E073	-27254
chr12	57939511	57941533	E073	-772
chr12	57943248	57944621	E073	943
chr12	57944681	57944857	E073	2376
chr12	57944886	57945001	E073	2581
chr12	57945065	57945105	E073	2760
chr12	57945115	57945274	E073	2810
chr12	57945433	57945560	E073	3128
chr12	57945589	57945751	E073	3284
chr12	57945845	57945940	E073	3540
chr12	57947293	57947404	E073	4988
chr12	57984184	57986177	E073	41879
chr12	57912852	57915051	E074	-27254
chr12	57939511	57941533	E074	-772
chr12	57943248	57944621	E074	943
chr12	57944681	57944857	E074	2376
chr12	57984184	57986177	E074	41879
chr12	57912852	57915051	E081	-27254
chr12	57943248	57944621	E081	943
chr12	57944681	57944857	E081	2376
chr12	57944886	57945001	E081	2581
chr12	57945065	57945105	E081	2760
chr12	57945115	57945274	E081	2810
chr12	57945433	57945560	E081	3128
chr12	57945589	57945751	E081	3284
chr12	57945845	57945940	E081	3540
chr12	57947293	57947404	E081	4988
chr12	57984184	57986177	E081	41879
chr12	57912852	57915051	E082	-27254
chr12	57939511	57941533	E082	-772
chr12	57943248	57944621	E082	943
chr12	57944681	57944857	E082	2376
chr12	57944886	57945001	E082	2581
chr12	57945065	57945105	E082	2760
chr12	57945115	57945274	E082	2810
chr12	57945433	57945560	E082	3128
chr12	57945589	57945751	E082	3284
chr12	57945845	57945940	E082	3540
chr12	57947293	57947404	E082	4988
chr12	57984184	57986177	E082	41879